You seem confused why GitHub did what they did. In the US there is something called "US Export Law", the law includes declarations that makes companies unable to sell services/goods to certain countries (which spoiler, Iran is part of that list).
The law itself is not illegal, as the lawmakers have created and enacted that law. It's the opposite, the law is declaring what's illegal.
So, if GitHub doesn't ban users from Iran, they are breaking the law in the US.
Hope this clears up any misunderstanding on how things work.
"the law includes declarations that makes companies unable to sell services/goods to certain countries" is not the same as "if GitHub doesn't ban users from Iran, they are breaking the law".
GitHub could comply with the law without completely banning users who access their service from Iran, e.g. by making their website unavailable for Iranian IPs or by making paid features unavailable.
IANAL and I'm not 100% confident on my knowledge around the export laws in the US, as I've only have to deal with that mess once in my lifetime.
But, if the CEO of GitHub (Nat Friedman) claims that they "do no more than what is required by the law" and end up banning a user, my understanding is that the lawyers are GitHub and Microsoft have made the judgement that banning users are a must, simply restricting them temporary is not enough.
Again, I think export embargoes are shit and don't necessarily agree with the calls that GitHub/Microsoft did, but trying to understand the side they are coming from here.
Who knows, probably? For the rest of the "Does X block Y if Y is in Iran|Other embargoed country" questions, the answers are either A) Yes, you'll get banned or B) No, they haven't thought of that yet, but they'll add banning as soon as they figure it out, as the law requires it.
The law itself is not illegal, as the lawmakers have created and enacted that law. It's the opposite, the law is declaring what's illegal.
So, if GitHub doesn't ban users from Iran, they are breaking the law in the US.
Hope this clears up any misunderstanding on how things work.